| IPO-package | Automated Optimization of Untargeted Metabolomics LC-MS Data Processing | 
| attachList | Attaching one list at the end of another | 
| calcPPS | Calculation of a peak picking score (PPS) by using natural, stable 13C isotopes | 
| calculateXcmsSet | Calculation of an xcmsSet-Object | 
| combineParams | Combining two lists of parameters together. | 
| createModel | Creating a response surface model. | 
| decode | En-/decodes values to/from ranges of -1 to 1. | 
| decodeAll | En-/decodes values to/from ranges of -1 to 1. | 
| encode | En-/decodes values to/from ranges of -1 to 1. | 
| findIsotopes.CAMERA | Identification of Isotopes using the package CAMERA. | 
| findIsotopes.IPO | Identification of 13C isotopes | 
| getBbdParameter | Creates a Box-Behnken Design of experiment | 
| getCcdParameter | Creates a Central-Composite Design of experiment | 
| getDefaultRetCorCenterSample | Gets the index of the sample with most peaks in it. | 
| getDefaultRetGroupStartingParams | Gives a List of parameters for xcms-methods retcor.obiwarp or retcor.loess and group.density which are optimized by default | 
| getDefaultXcmsSetStartingParams | Creates a List of parameters for xcms-methods xcmsSet.findPeak which are optimized by default | 
| getNormalizedResponse | It combines Retention time Correction Scores (RCS) and Grouping Scores (GS) | 
| getRGTVValues | Calculation of values used for a Retention time correction and Grouping Target Value (RGTV) | 
| IPO | Automated Optimization of Untargeted Metabolomics LC-MS Data Processing | 
| optimizeRetGroup | Optimization for parameters for retention time correction and grouping | 
| optimizeXcmsSet | Optimisation of peak picking parameters by using natural, stable 13C isotopes | 
| toMatrix | Converts an array into a matrix | 
| typeCastParams | Splits parameters into those which should be optimized and those which are fixed. | 
| writeParamsTable | Writes XCMS settings to a file. | 
| writeRScript | Prints an R-script to the screen which can be used for xcms processing |